Tagged Questions

Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ...

I have several .ab1 files generated from Chromas. I want to merge all of them into a single FASTA sequence file. How can I do this in an automated way?
Note that I don't have Chromas installed (the ...

I am attempting to validate existence of a transcript using 40 cycle qPCR. I designed primers for a unique feature of this transcript, and also designed primers for a sequence in the transcript that ...

Are there respectable scientific journals for publishing models of protein-protein interactions obtained by docking simulations? I would also discuss the biological significance of the particular mode ...

I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, ...

How to extract protein sequences from a GBK(GenBank) file without scripting?
I know that writting a script using BioPerl or Biopython can do this, but it is not elegant and daunting to beginners and ...

There are many hydrophobicity scales for protein analysis.
Broadly, I gather the differences between them are from the experimental method to acquire the data and the normalisation (or lack thereof) ...

I created an algorithm to generate SNPs for random people of different descents - based on HapMap data. While this works good, there is something else I want to take into consideration. So if a SNP ...

There is an attribute defined as DP (Total Depth) in VCF file format. For example, http://www.1000genomes.org/node/101.
What does this attribute mean? If I get a value of like DP=128. How can be that ...

I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching).
I am curious about the "regular expression (regex)" (pattern/motif) ...

I have a postgraduate degree in computer science, and I wish to undertake research in bioinformatics. I had chemistry but no biology in high school. I have read bioinformatics books like "biological ...

I am trying to figure out how to find the number of child terms associated with a specific Gene Ontology (GO) term using QuickGO, without just counting the amount of terms in a list. For example when ...

I am just starting to learn to use bioinformatics tools. My university has a limited and expensive bioinformatics team, so I'm mostly on my own except for big questions.
I am planning to use GATK to ...

I design my primers in Primer3PLUS and analyze them in Oligoanalyzer3.1, A big problem that I have this is that I got very nice output in NCBI-Primer BLAST for their specificity but a very negative ΔG ...

I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days ...

I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data ...

I began working with panTro3 assembly of the UCSC. This assembly corresponds to CGSC Build 2.1.3. See here: https://genome.ucsc.edu/FAQ/FAQreleases.html
Now, I have to cross annotations with ENSEMBL ...

Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example?
I am new to bioinformatics, and I have not found any conclusive ...

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.).
The question that I have is: How do you know ...

I'm about to start a bioinformatics research project but I haven't any biological background.
I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like ...

I have attempted a few searches for a list of origins of replication for plasmids in E. coli, but I was only able to find a list of origins, but not their individual sequences. The available plasmid ...